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. 2022 Jun 8;6(6):e406.
doi: 10.1002/pld3.406. eCollection 2022 Jun.

First Plant Cell Atlas symposium report

Selena L Rice  1 , Elena Lazarus  1 , Christopher Anderton  2 , Kenneth Birnbaum  3 , Jennifer Brophy  4 , Benjamin Cole  5 , Diane Dickel  6 , David Ehrhardt  1 , Noah Fahlgren  7 , Margaret Frank  8 , Elizabeth Haswell  9 , Shao-Shan Carol Huang  3 , Samuel Leiboff  10 , Marc Libault  11 , Marisa S Otegui  12 , Nicholas Provart  13 , R Glen Uhrig  14 , Seung Y Rhee  1 ; Plant Cell Atlas Consortium
Affiliations

First Plant Cell Atlas symposium report

Selena L Rice et al. Plant Direct. .

Abstract

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber-infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell-type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user-friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community-supported data evaluation metrics, accelerating plant research necessary for human and environmental health.

Keywords: data science; live imaging; plant cell atlas; proteomics; single‐cell sequencing; spatial transcriptomics.

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Conflict of interest statement

The Authors did not report any conflict of interest.

References

    1. Cole, B. , Bergmann, D. , Blaby‐Haas, C. E. , Blaby, I. K. , Bouchard, K. E. , Brady, S. M. , Ciobanu, D. , Coleman‐Derr, D. , Leiboff, S. , Mortimer, J. C. , Nobori, T. , Rhee, S. Y. , Schmutz, J. , Simmons, B. A. , Singh, A. K. , Sinha, N. , Vogel, J. P. , O'Malley, R. C. , Visel, A. , & Dickel, D. E. (2021). Plant single‐cell solutions for energy and the environment. Communications Biology, 4(1), 962. 10.1038/s42003-021-02477-4 - DOI - PMC - PubMed
    1. Cooper, L. , Meier, A. , Laporte, M.‐A. , Elser, J. L. , Mungall, C. , Sinn, B. T. , Cavaliere, D. , Carbon, S. , Dunn, N. A. , Smith, B. , Qu, B. , Preece, J. , Zhang, E. , Todorovic, S. , Gkoutos, G. , Doonan, J. H. , Stevenson, D. W. , Arnaud, E. , & Jaiswal, P. (2018). The Planteome database: An integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Research, 46, D1168–D1180. 10.1093/nar/gkx1152 - DOI - PMC - PubMed
    1. Cuperus, J. T. (2021). Single‐cell genomics in plants: Current state, future directions, and hurdles to overcome. Plant Physiology, 188, 749–755. 10.1093/plphys/kiab478 - DOI - PMC - PubMed
    1. Di Tommaso, P. , Chatzou, M. , Floden, E. W. , Barja, P. P. , Palumbo, E. , & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35, 316–319. 10.1038/nbt.3820 - DOI - PubMed
    1. Goodstein, D. M. , Shu, S. , Howson, R. , Neupane, R. , Hayes, R. D. , Fazo, J. , Mitros, T. , Dirks, W. , Hellsten, U. , Putnam, N. , & Rokhsar, D. S. (2012). Phytozome: A comparative platform for green plant genomics. Nucleic Acids Research, 40, D1178–D1186. 10.1093/nar/gkr944 - DOI - PMC - PubMed